It seems it is not possible. Sad
I've checked AIR and Java bridge, but that only supports Flex and I'm developing in HTML/JS. Python solutions also didn't work. Any ideas?
Do you have some library (in native code or Java or whatever) that actually knows how to communicate over the USB driver using the iPod transmission protocol? As far as I know - this protocol is not public knowlege. That being said - there is no direct AIR to USB communication channel. However, if you had access to it through other libraries, you could create a Native Application (new in AIR 2.0 and can be written using HTML just like a regular AIR application) that contained the USB <-> iPod communication layer and do the rest of your application management in AIR.
Hope that helps.
BTW - If you figure something out..let me know...I have been wanting to write something like this as well!